[2023-06-13 10:49:49,954] [INFO] DFAST_QC pipeline started.
[2023-06-13 10:49:49,956] [INFO] DFAST_QC version: 0.5.7
[2023-06-13 10:49:49,956] [INFO] DQC Reference Directory: /var/lib/cwl/stgce2123d9-deaf-414c-a36a-665a5c16a835/dqc_reference
[2023-06-13 10:49:51,832] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-13 10:49:51,833] [INFO] Task started: Prodigal
[2023-06-13 10:49:51,833] [INFO] Running command: gunzip -c /var/lib/cwl/stg59f8596c-3bd8-4a4f-8fc5-ded321698dc6/GCA_938014185.1_SRR8114027_bin.73_CONCOCT_v1.1_MAG_genomic.fna.gz | prodigal -d GCA_938014185.1_SRR8114027_bin.73_CONCOCT_v1.1_MAG_genomic.fna/cds.fna -a GCA_938014185.1_SRR8114027_bin.73_CONCOCT_v1.1_MAG_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-13 10:50:12,366] [INFO] Task succeeded: Prodigal
[2023-06-13 10:50:12,366] [INFO] Task started: HMMsearch
[2023-06-13 10:50:12,367] [INFO] Running command: hmmsearch --tblout GCA_938014185.1_SRR8114027_bin.73_CONCOCT_v1.1_MAG_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgce2123d9-deaf-414c-a36a-665a5c16a835/dqc_reference/reference_markers.hmm GCA_938014185.1_SRR8114027_bin.73_CONCOCT_v1.1_MAG_genomic.fna/protein.faa > /dev/null
[2023-06-13 10:50:12,646] [INFO] Task succeeded: HMMsearch
[2023-06-13 10:50:12,648] [INFO] Found 6/6 markers.
[2023-06-13 10:50:12,686] [INFO] Query marker FASTA was written to GCA_938014185.1_SRR8114027_bin.73_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta
[2023-06-13 10:50:12,687] [INFO] Task started: Blastn
[2023-06-13 10:50:12,687] [INFO] Running command: blastn -query GCA_938014185.1_SRR8114027_bin.73_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stgce2123d9-deaf-414c-a36a-665a5c16a835/dqc_reference/reference_markers.fasta -out GCA_938014185.1_SRR8114027_bin.73_CONCOCT_v1.1_MAG_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 10:50:13,318] [INFO] Task succeeded: Blastn
[2023-06-13 10:50:13,327] [INFO] Selected 29 target genomes.
[2023-06-13 10:50:13,327] [INFO] Target genome list was writen to GCA_938014185.1_SRR8114027_bin.73_CONCOCT_v1.1_MAG_genomic.fna/target_genomes.txt
[2023-06-13 10:50:13,332] [INFO] Task started: fastANI
[2023-06-13 10:50:13,332] [INFO] Running command: fastANI --query /var/lib/cwl/stg59f8596c-3bd8-4a4f-8fc5-ded321698dc6/GCA_938014185.1_SRR8114027_bin.73_CONCOCT_v1.1_MAG_genomic.fna.gz --refList GCA_938014185.1_SRR8114027_bin.73_CONCOCT_v1.1_MAG_genomic.fna/target_genomes.txt --output GCA_938014185.1_SRR8114027_bin.73_CONCOCT_v1.1_MAG_genomic.fna/fastani_result.tsv --threads 1
[2023-06-13 10:50:28,835] [INFO] Task succeeded: fastANI
[2023-06-13 10:50:28,836] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgce2123d9-deaf-414c-a36a-665a5c16a835/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-13 10:50:28,836] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgce2123d9-deaf-414c-a36a-665a5c16a835/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-13 10:50:28,855] [INFO] Found 23 fastANI hits (0 hits with ANI > threshold)
[2023-06-13 10:50:28,855] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-13 10:50:28,855] [INFO] DFAST Taxonomy check final result
--------------------------------------------------------------------------------
organism_name	strain	accession	taxid	species_taxid	relation_to_type	validated	ani	matched_fragments	total_fragments	ani_threshold	status
Prevotella mizrahii	strain=LKV-178-WT-2A	GCA_009695775.1	2606637	2606637	type	True	80.831	178	1084	95	below_threshold
Prevotella lacticifex	strain=R5019	GCA_019973375.1	2854755	2854755	type	True	79.819	182	1084	95	below_threshold
Prevotella fusca	strain=W1435	GCA_018128145.1	589436	589436	type	True	76.8497	61	1084	95	below_threshold
Prevotella fusca	strain=W1435	GCA_001262015.1	589436	589436	type	True	76.8374	59	1084	95	below_threshold
Prevotella vespertina	strain=A2879	GCA_009728485.1	2608404	2608404	type	True	76.8017	53	1084	95	below_threshold
Hallella faecis	strain=CLA-AA-H145	GCA_018789675.1	2841596	2841596	type	True	76.7804	125	1084	95	below_threshold
Prevotella stercorea	strain=DSM 18206	GCA_000235885.1	363265	363265	suspected-type	True	76.7324	94	1084	95	below_threshold
Prevotella falsenii	strain=JCM 15124	GCA_000613945.1	515414	515414	type	True	76.7253	56	1084	95	below_threshold
Prevotella scopos	strain=W2052	GCA_018127785.1	589437	589437	type	True	76.6408	60	1084	95	below_threshold
Prevotella dentasini	strain=JCM 15908	GCA_000614065.1	589537	589537	type	True	76.6158	94	1084	95	below_threshold
Prevotella dentalis	strain=DSM 3688	GCA_000220215.1	52227	52227	type	True	76.6133	112	1084	95	below_threshold
Prevotella copri	strain=DSM 18205	GCA_009495405.1	165179	165179	suspected-type	True	76.609	95	1084	95	below_threshold
Prevotella denticola	strain=NCTC13067	GCA_900454835.1	28129	28129	type	True	76.6009	88	1084	95	below_threshold
Prevotella denticola	strain=DSM 20614	GCA_000421205.1	28129	28129	type	True	76.575	86	1084	95	below_threshold
Prevotella scopos	strain=W2052	GCA_001683355.1	589437	589437	type	True	76.5627	59	1084	95	below_threshold
Prevotella dentalis	strain=DSM 3688	GCA_000242335.3	52227	52227	type	True	76.5318	110	1084	95	below_threshold
Hallella seregens	strain=ATCC 51272	GCA_000518545.1	52229	52229	type	True	76.4611	113	1084	95	below_threshold
Prevotella multiformis	strain=DSM 16608	GCA_000191065.1	282402	282402	type	True	76.4502	100	1084	95	below_threshold
Prevotella buccae	strain=ATCC 33574	GCA_000184945.1	28126	28126	type	True	76.3965	115	1084	95	below_threshold
Prevotella brevis	strain=ATCC 19188	GCA_000621725.1	83231	83231	type	True	76.3953	68	1084	95	below_threshold
Prevotella bergensis	strain=DSM 17361	GCA_000160535.1	242750	242750	type	True	76.3463	64	1084	95	below_threshold
Xylanibacter rodentium	strain=PROD	GCA_013166575.1	2736289	2736289	type	True	76.1608	62	1084	95	below_threshold
Prevotella ruminicola	strain=ATCC 19189	GCA_900108375.1	839	839	type	True	75.96	60	1084	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-13 10:50:28,863] [INFO] DFAST Taxonomy check result was written to GCA_938014185.1_SRR8114027_bin.73_CONCOCT_v1.1_MAG_genomic.fna/tc_result.tsv
[2023-06-13 10:50:28,864] [INFO] ===== Taxonomy check completed =====
[2023-06-13 10:50:28,864] [INFO] ===== Start completeness check using CheckM =====
[2023-06-13 10:50:28,864] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgce2123d9-deaf-414c-a36a-665a5c16a835/dqc_reference/checkm_data
[2023-06-13 10:50:28,865] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-13 10:50:28,912] [INFO] Task started: CheckM
[2023-06-13 10:50:28,912] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_938014185.1_SRR8114027_bin.73_CONCOCT_v1.1_MAG_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_938014185.1_SRR8114027_bin.73_CONCOCT_v1.1_MAG_genomic.fna/checkm_input GCA_938014185.1_SRR8114027_bin.73_CONCOCT_v1.1_MAG_genomic.fna/checkm_result
[2023-06-13 10:51:26,356] [INFO] Task succeeded: CheckM
[2023-06-13 10:51:26,358] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 98.96%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-13 10:51:26,381] [INFO] ===== Completeness check finished =====
[2023-06-13 10:51:26,381] [INFO] ===== Start GTDB Search =====
[2023-06-13 10:51:26,382] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_938014185.1_SRR8114027_bin.73_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta)
[2023-06-13 10:51:26,382] [INFO] Task started: Blastn
[2023-06-13 10:51:26,382] [INFO] Running command: blastn -query GCA_938014185.1_SRR8114027_bin.73_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stgce2123d9-deaf-414c-a36a-665a5c16a835/dqc_reference/reference_markers_gtdb.fasta -out GCA_938014185.1_SRR8114027_bin.73_CONCOCT_v1.1_MAG_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 10:51:27,230] [INFO] Task succeeded: Blastn
[2023-06-13 10:51:27,237] [INFO] Selected 28 target genomes.
[2023-06-13 10:51:27,237] [INFO] Target genome list was writen to GCA_938014185.1_SRR8114027_bin.73_CONCOCT_v1.1_MAG_genomic.fna/target_genomes_gtdb.txt
[2023-06-13 10:51:27,249] [INFO] Task started: fastANI
[2023-06-13 10:51:27,249] [INFO] Running command: fastANI --query /var/lib/cwl/stg59f8596c-3bd8-4a4f-8fc5-ded321698dc6/GCA_938014185.1_SRR8114027_bin.73_CONCOCT_v1.1_MAG_genomic.fna.gz --refList GCA_938014185.1_SRR8114027_bin.73_CONCOCT_v1.1_MAG_genomic.fna/target_genomes_gtdb.txt --output GCA_938014185.1_SRR8114027_bin.73_CONCOCT_v1.1_MAG_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-13 10:51:42,132] [INFO] Task succeeded: fastANI
[2023-06-13 10:51:42,164] [INFO] Found 26 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-13 10:51:42,165] [INFO] GTDB search result
--------------------------------------------------------------------------------
accession	gtdb_species	ani	matched_fragments	total_fragments	gtdb_taxonomy	ani_circumscription_radius	mean_intra_species_ani	min_intra_species_ani	mean_intra_species_af	min_intra_species_af	num_clustered_genomes	status
GCA_002480935.1	s__Prevotella sp002480935	97.6064	540	1084	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	98.13	97.58	0.84	0.77	8	conclusive
GCA_002481295.1	s__Prevotella sp002481295	77.6565	129	1084	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	97.83	96.70	0.87	0.78	4	-
GCA_900319905.1	s__Prevotella sp900319905	77.4774	117	1084	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	98.87	98.44	0.89	0.87	7	-
GCA_900314195.1	s__Prevotella sp900314195	77.3425	78	1084	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	100.00	100.00	0.99	0.99	2	-
GCA_900199655.1	s__Prevotella sp900199655	77.1935	129	1084	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	99.91	99.91	0.98	0.98	2	-
GCF_009495355.1	s__Prevotella sp900313215	77.1681	99	1084	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	97.34	96.92	0.81	0.74	15	-
GCA_900315635.1	s__Prevotella sp900315635	77.0565	118	1084	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	99.69	99.39	0.92	0.85	3	-
GCA_900316565.1	s__Prevotella sp900316565	76.8417	119	1084	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	97.52	96.90	0.84	0.79	9	-
GCF_018789675.1	s__Prevotella sp002300055	76.7614	126	1084	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	99.15	99.02	0.92	0.90	6	-
GCF_018128065.1	s__Prevotella sp000467895	76.7607	58	1084	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	97.71	96.42	0.91	0.83	4	-
GCA_002439605.1	s__Prevotella sp002439605	76.6261	77	1084	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	99.57	99.57	0.81	0.81	2	-
GCF_000614065.1	s__Prevotella dentasini	76.6158	94	1084	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002437285.1	s__Prevotella sp002437285	76.5655	117	1084	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	99.68	99.38	0.93	0.88	13	-
GCA_902786565.1	s__Prevotella sp902786565	76.5626	91	1084	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	98.07	98.05	0.87	0.85	3	-
GCA_002353485.1	s__Prevotella sp002353485	76.5555	71	1084	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	97.45	97.45	0.90	0.90	2	-
GCF_000518545.1	s__Prevotella seregens	76.4611	113	1084	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	98.68	98.64	0.90	0.90	3	-
GCA_017428055.1	s__Prevotella sp017428055	76.4213	66	1084	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	98.50	98.50	0.89	0.89	2	-
GCF_000184945.1	s__Prevotella buccae	76.3965	115	1084	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	98.38	98.24	0.91	0.87	7	-
GCA_017442825.1	s__Prevotella sp017442825	76.2843	63	1084	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900315565.1	s__Prevotella sp900315565	76.2609	123	1084	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	98.12	96.25	0.91	0.84	3	-
GCA_905234265.1	s__Prevotella sp905234265	76.23	76	1084	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902769705.1	s__Prevotella sp902769705	76.2173	87	1084	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	96.61	96.53	0.84	0.80	3	-
GCA_902781315.1	s__Prevotella sp902781315	76.1863	101	1084	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	96.55	96.55	0.79	0.79	2	-
GCA_002342415.1	s__Prevotella sp002342415	76.107	76	1084	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002353525.1	s__Prevotella sp002353525	76.0041	80	1084	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002305235.1	s__Prevotella sp002305235	75.9833	76	1084	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-13 10:51:42,167] [INFO] GTDB search result was written to GCA_938014185.1_SRR8114027_bin.73_CONCOCT_v1.1_MAG_genomic.fna/result_gtdb.tsv
[2023-06-13 10:51:42,167] [INFO] ===== GTDB Search completed =====
[2023-06-13 10:51:42,172] [INFO] DFAST_QC result json was written to GCA_938014185.1_SRR8114027_bin.73_CONCOCT_v1.1_MAG_genomic.fna/dqc_result.json
[2023-06-13 10:51:42,173] [INFO] DFAST_QC completed!
[2023-06-13 10:51:42,173] [INFO] Total running time: 0h1m52s